It is not clear from the function documentation of run_de if it compares one group to all others or to each other group. The authors of scran make a good point that it should be multiple pairwise comparisons to avoid a bias being caused by a dominant cell type.
We deliberately use pairwise comparisons rather than comparing each cluster to the average of all other cells. The latter approach is sensitive to the population composition, which introduces an element of unpredictability to the marker sets due to variation in cell type abundances.
Source: Orchestrating Single Cell Analysis, Chapter 6.
It is not clear from the function documentation of
run_deif it compares one group to all others or to each other group. The authors of scran make a good point that it should be multiple pairwise comparisons to avoid a bias being caused by a dominant cell type.Source: Orchestrating Single Cell Analysis, Chapter 6.